My Recommendations (some of the stuff I'd recommend like BOS and WOTOR are already listed by others so I'll omit them):

Improved AI by stoffe
*all reskins* by Darth Jaden
Darth Nihilus - Lord of Hunger by Dewton
Sith Officers to Imperial Officers by ?
M4-78RP and all patches and movies by DStoney
Bastilla Improvement Project by ? (yes I know this gives her a boob job, but it also improves her lip model and fixes her appearance in certain armors and clothes so bear with me...)
TSL:UR Final by zbyl2

I want to say USM but that mod needs some work.

As of 3/14/10, TSL is restored. The Sith Lords Restored Content Modification by Stoney and Zbyl has been finished and can be downloaded here.